The development of pore overpressure beneath high-crystallinity, low-permeability magma plugs is often inferred to be the cause of hazardous vulcanian explosions at many active arc volcanoes. Using a combination of porosity and permeability measurements and X-ray micro-tomographic reconstructions of ballistic bombs from the 2004–2010 explosions of Galeras volcano, Colombia, we document the micro-structural changes of the permeable porous network in high-crystallinity andesitic magma plugs resulting from natural viscous densification. Mean pore volumes, mean pore throat areas and the volumetric number density of connected pores and throats decline as connected porosity and permeability decrease. The mean pore coordination number and the volumetric number density of disconnected (isolated) voids also tend to decrease with decreasing porosity and permeability. The variance in pore volume and throat area decrease as a result of this densification process and tortuosity decreases slightly, demonstrating that the range of scales of structures performing gas transfer is reduced and the porous network undergoes viscous re-organisation. The reduction in tortuosity illustrates how permeability is reduced but maintained to low connected porosities, allowing plug formation to occur without creating large-scale pore overpressure within the plug. We characterise the relationships between key topological parameters and between connected porosity and permeability to facilitate future modelling of this process. Micro-tomographic reconstructions of a breadcrust bomb rind indicate that a deeper region with large pores, large throats, high pore volume and throat area variance and high tortuosity exists below low-permeability plugs, and this could represent a likely area for explosion-driving overpressure to develop following plug densification. A comparison of our porous micro-structure data with existing crystal micro-textures and glass volatile data from the same samples suggests that the average magma ascent and decompression rates ultimately control the efficiency of magma densification, the final plug permeability and the extent of degassing of the melt phase.